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    SC5D sterol-C5-desaturase [ Homo sapiens (human) ]

    Gene ID: 6309, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SC5Dprovided by HGNC
    Official Full Name
    sterol-C5-desaturaseprovided by HGNC
    Primary source
    HGNC:HGNC:10547
    See related
    Ensembl:ENSG00000109929 MIM:602286; AllianceGenome:HGNC:10547
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ERG3; S5DES; SC5DL
    Summary
    This gene encodes an enzyme of cholesterol biosynthesis. The encoded protein catalyzes the conversion of lathosterol into 7-dehydrocholesterol. Mutations in this gene have been associated with lathosterolosis. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in liver (RPKM 29.7), prostate (RPKM 24.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SC5D in Genome Data Viewer
    Location:
    11q23.3-q24.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (121292771..121313410)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (121317829..121338469)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (121163480..121184119)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:121117070-121117656 Neighboring gene NANOG hESC enhancer GRCh37_chr11:121119641-121120200 Neighboring gene ribosomal protein S4X pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:121165985-121166526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:121166527-121167069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5646 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:121243330-121244107 Neighboring gene bone morphogenetic protein receptor type 1A pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121260007-121260508 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121260509-121261008 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:121276805-121277684 Neighboring gene NANOG hESC enhancer GRCh37_chr11:121277972-121278473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:121297351-121297863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4003 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5653 Neighboring gene SORL1 antisense RNA 1 Neighboring gene sortilin related receptor 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Lathosterolosis. Adam MP, et al. , 1993. PMID 38060690
    2. Evidence that liver microsomes of human neonates desaturate essential fatty acids. Poisson JP, et al. Biochim Biophys Acta, 1993 Apr 7. PMID 8466936
    3. Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase. Matsushima M, et al. Cytogenet Cell Genet, 1996. PMID 8976377
    4. Relationship between Body Mass Index, C-Peptide, and Delta-5-Desaturase Enzyme Activity Estimates in Adult Males. Pickens CA, et al. PLoS One, 2016. PMID 27023786, Free PMC Article
    5. 7-Dehydrocholesterol is an endogenous suppressor of ferroptosis. Freitas FP, et al. Nature, 2024 Feb. PMID 38297129

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The relationship between C-peptide concentrations and D5D enzyme activity estimates remained significant after adjusting for body mass index, waist circumference, and TNF-alpha.
      Title: Relationship between Body Mass Index, C-Peptide, and Delta-5-Desaturase Enzyme Activity Estimates in Adult Males.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. The EGR3 may not play a major role in schizophrenia susceptibility in the Chinese Han population.
      Title: No association between EGR gene family polymorphisms and schizophrenia in the Chinese population.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Lathosterolosis
    MedGen: C1846421 OMIM: 607330 GeneReviews: Lathosterolosis
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C-5 sterol desaturase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables C-5 sterol desaturase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables delta7-sterol 5(6)-desaturase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cholesterol biosynthetic process via desmosterol TAS
    Traceable Author Statement
    more info
    		  
    involved_in cholesterol biosynthetic process via lathosterol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cholesterol biosynthetic process via lathosterol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cholesterol biosynthetic process via lathosterol TAS
    Traceable Author Statement
    more info
    		  
    involved_in negative regulation of ferroptosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    lathosterol oxidase
    Names
    3beta-hydroxysteroid-delta5-desaturase
    C-5 sterol desaturase
    delta(7)-sterol 5(6)-desaturase
    delta(7)-sterol 5-desaturase
    delta(7)-sterol C5(6)-desaturase
    fungal ERG3, delta-5-desaturase-like
    lathosterol 5-desaturase
    lathosterol dehydrogenase
    sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like
    NP_001020127.1
    NP_008849.2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009446.1 RefSeqGene

      Range
      5093..25732
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001024956.3 → NP_001020127.1  lathosterol oxidase

      See identical proteins and their annotated locations for NP_001020127.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' exon compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AP002959, BC012333
      Consensus CDS
      CCDS8435.1
      UniProtKB/Swiss-Prot
      O00119, O75845, Q6GTM5, Q9UK15
      Related
      ENSP00000376539.2, ENST00000392789.2
      Conserved Domains (1) summary
      COG3000
      Location:34 → 257
      ERG3; Sterol desaturase/sphingolipid hydroxylase, fatty acid hydroxylase superfamily [Lipid transport and metabolism]

    2. NM_006918.5 → NP_008849.2  lathosterol oxidase

      See identical proteins and their annotated locations for NP_008849.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK223141, AP002959
      Consensus CDS
      CCDS8435.1
      UniProtKB/Swiss-Prot
      O00119, O75845, Q6GTM5, Q9UK15
      Related
      ENSP00000264027.4, ENST00000264027.9
      Conserved Domains (1) summary
      COG3000
      Location:34 → 257
      ERG3; Sterol desaturase/sphingolipid hydroxylase, fatty acid hydroxylase superfamily [Lipid transport and metabolism]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      121292771..121313410
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      121317829..121338469
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75845.2 GenPept UniProtKB/Swiss-Prot:O75845

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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